The Dundee striker was allegedly filmed launching the canister back into the away stand housing St Johnstone fans after it had been thrown onto the pitchside in the aftermath of the Perth side’s opening goal in the 2-0 Premier Sports Cup quarter-final victory.
The on-loan Celtic hitman issued an apology following the incident, insisting he was only trying to knock the flare off the pitch and had no intention of it travelling into the away crowd as they chanted abuse at the Scottish international.
Griffiths said: “It was regrettable that the pyrotechnic ended up back in the stand as my intention was just to remove it from the pitch.
“Having just lost a goal I was eager to get the match restarted as quickly as possible and I would like to apologise for any distress caused by this action.”
It is not believed anyone was injured, however, police have now charged Griffiths over the incident, with an SFA ban also on the cards after the compliance officer launched an investigation into the footage.
A Police Scotland spokesperson said: "Police Scotland can confirm that a 31-year-old man has been charged in relation to culpable and reckless conduct, following an incident at Dens Park, Dundee, on Wednesday, 22 September.
"A report will be submitted to the Procurator Fiscal."
Dundee branded the incident “regrettable” in a statement which read: "Dundee Football Club and Leigh Griffiths would like to address a regrettable incident which occurred during last night’s Premier Sports Cup tie with St. Johnstone at the Kilmac Stadium.
"Following the opening goal a smoke generator, amongst other items, was thrown onto the park by the visiting supporters.
"This pyrotechnic ended up back in the stand as Leigh kicked it to remove it from the field of play."
The club have said they will make no further comment at this moment in time.
Griffiths signed for Dundee on loan from Celtic on the final day of the transfer window and has yet to score in three appearances. The former Hibs striker also previously played for the Dark Blues in the 2009/2010 season.